Application of 1H NMR chemical shifts to measure the quality of protein structures

Abstract

We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When applied to NMR structures, agreement between calculated and observed shifts is generally of the same quality as that for crystal structures of resolution between 2.0 and 3.0 A. There is a rather weak correlation between standard deviation (SD) and the number of NMR constraints per residue, but none with the root-mean-square deviation of one NMR structure from another. Where minimised averaged structures are present, they have about the same SD as the population from which they were taken. Refinement methods such as energy minimisation and the use of relaxation matrices and back calculation produce little or no improvement in SD. The calculation has several applications, particularly as an independent means of measuring the quality of a structure (either in the crystal or in solution), and in identifying possible assignment errors.